Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 10:56:14.930609313 +0000 +++ b2/build.log 2024-05-09 11:03:54.175069464 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 8 22:28:35 -12 2024 -I: pbuilder-time-stamp: 1715250515 +I: Current time: Thu Jun 12 07:19:18 +14 2025 +I: pbuilder-time-stamp: 1749662358 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3477194/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 11 17:19 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ccd49cc0ccb748d8ab152b236ad8b17d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3477194' - PS1='# ' - PS2='> ' + INVOCATION_ID=b3f5bdbd42444cd887eb7af37bc32b1f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3395150 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fADRoSis/pbuilderrc_EXea --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fADRoSis/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fADRoSis/pbuilderrc_JqSA --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fADRoSis/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3477194/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 31 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] -Fetched 21.2 MB in 1s (18.5 MB/s) +Fetched 21.2 MB in 0s (123 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -293,7 +325,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -364,7 +400,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make all-am make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' @@ -405,9 +441,9 @@ Single-end simulation -Total CPU time used: 0.130669 +Total CPU time used: 0.041469 -The random seed for the run: 1715250660 +The random seed for the run: 1749662397 Parameters Settings number of flow cycles: 100 @@ -438,9 +474,9 @@ Paired-end simulation -Total CPU time used: 0.10799 +Total CPU time used: 0.031912 -The random seed for the run: 1715250661 +The random seed for the run: 1749662397 Parameters Settings number of flow cycles: 100 @@ -476,9 +512,9 @@ Paired-end simulation -Total CPU time used: 0.113152 +Total CPU time used: 0.035413 -The random seed for the run: 1715250661 +The random seed for the run: 1749662397 Parameters Settings number of flow cycles: 200 @@ -514,9 +550,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 20.4766 +Total CPU time used: 6.78368 -The random seed for the run: 1715250662 +The random seed for the run: 1749662397 Parameters Settings number of flow cycles: 100 @@ -547,9 +583,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 17.377 +Total CPU time used: 5.42796 -The random seed for the run: 1715250695 +The random seed for the run: 1749662404 Parameters Settings number of flow cycles: 100 @@ -582,7 +618,7 @@ Single-end simulation -Total CPU time used: 0.129607 +Total CPU time used: 0.040818 The random seed for the run: 777 @@ -615,7 +651,7 @@ Single-end simulation -Total CPU time used: 0.125425 +Total CPU time used: 0.040953 The random seed for the run: 777 @@ -649,9 +685,9 @@ Single-end simulation -Total CPU time used: 0.221337 +Total CPU time used: 0.06485 -The random seed for the run: 1715250721 +The random seed for the run: 1749662410 Parameters Settings fold of read coverage: 10X @@ -681,9 +717,9 @@ Single-end simulation -Total CPU time used: 0.229647 +Total CPU time used: 0.084298 -The random seed for the run: 1715250721 +The random seed for the run: 1749662410 Parameters Settings fold of read coverage: 20X @@ -711,9 +747,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.318752 +Total CPU time used: 0.122383 -The random seed for the run: 1715250721 +The random seed for the run: 1749662410 Parameters Settings fold of read coverage: 20X @@ -751,7 +787,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.148157 +Total CPU time used: 0.060275 The random seed for the run: 777 @@ -789,7 +825,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.147363 +Total CPU time used: 0.054068 The random seed for the run: 777 @@ -832,9 +868,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.48603 +Total CPU time used: 0.18986 -The random seed for the run: 1715250722 +The random seed for the run: 1749662410 Parameters Settings fold of read coverage: 50X @@ -868,9 +904,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 486.762 +Total CPU time used: 160.34 -The random seed for the run: 1715250723 +The random seed for the run: 1749662410 Parameters Settings # reads per amplion: 100 @@ -900,9 +936,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 255.616 +Total CPU time used: 93.9859 -The random seed for the run: 1715251432 +The random seed for the run: 1749662592 Parameters Settings # read pairs per amplion: 80 @@ -933,9 +969,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 185.562 +Total CPU time used: 62.0146 -The random seed for the run: 1715251825 +The random seed for the run: 1749662719 Parameters Settings # read pairs per amplion: 50 @@ -967,9 +1003,9 @@ Single-end Simulation -Total CPU time used: 0.133319 +Total CPU time used: 0.042587 -The random seed for the run: 1715252124 +The random seed for the run: 1749662791 Parameters used during run Read Length: 35 @@ -1001,9 +1037,9 @@ Single-end Simulation -Total CPU time used: 0.112429 +Total CPU time used: 0.034878 -The random seed for the run: 1715252124 +The random seed for the run: 1749662791 Parameters used during run Read Length: 50 @@ -1035,9 +1071,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.065022 +Total CPU time used: 0.024216 -The random seed for the run: 1715252124 +The random seed for the run: 1749662791 Parameters used during run Read Length: 150 @@ -1074,9 +1110,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.114837 +Total CPU time used: 0.039353 -The random seed for the run: 1715252124 +The random seed for the run: 1749662791 Parameters used during run Read Length: 100 @@ -1113,9 +1149,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.084665 +Total CPU time used: 0.02839 -The random seed for the run: 1715252125 +The random seed for the run: 1749662791 Parameters used during run Read Length: 100 @@ -1152,9 +1188,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.589278 +Total CPU time used: 0.251171 -The random seed for the run: 1715252125 +The random seed for the run: 1749662791 Parameters used during run Read Length: 100 @@ -1186,9 +1222,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 0.826937 +Total CPU time used: 0.308265 -The random seed for the run: 1715252126 +The random seed for the run: 1749662791 Parameters used during run Read Length: 100 @@ -1223,9 +1259,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 1.16481 +Total CPU time used: 0.458806 -The random seed for the run: 1715252127 +The random seed for the run: 1749662792 Parameters used during run Read Length: 100 @@ -1260,7 +1296,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.074686 +Total CPU time used: 0.026351 The random seed for the run: 777 @@ -1299,7 +1335,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.078641 +Total CPU time used: 0.025749 The random seed for the run: 777 @@ -1338,9 +1374,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.0897 +Total CPU time used: 0.03128 -The random seed for the run: 1715252131 +The random seed for the run: 1749662793 Parameters used during run Read Length: 100 @@ -1379,9 +1415,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.089597 +Total CPU time used: 0.028077 -The random seed for the run: 1715252132 +The random seed for the run: 1749662793 Parameters used during run Read Length: 75 @@ -1414,12 +1450,12 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j20 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' - /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' @@ -1469,13 +1505,13 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined +dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb'. +dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes @@ -1484,12 +1520,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3395150/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3477194 and its subdirectories -I: Current time: Wed May 8 22:56:13 -12 2024 -I: pbuilder-time-stamp: 1715252173 +I: removing directory /srv/workspace/pbuilder/3395150 and its subdirectories +I: Current time: Thu Jun 12 07:26:53 +14 2025 +I: pbuilder-time-stamp: 1749662813